Variant report

Variant	rs2306674
Chromosome Location	chr15:44198049-44198050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44190087..44193923-chr15:44195170..44198299,3	K562	blood:
2	chr15:44197183..44199224-chr15:44211558..44213453,2	MCF-7	breast:
3	chr15:44196106..44199754-chr15:44205350..44208904,3	K562	blood:

Variant related genes	Relation type
ENSG00000171877	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1008183	1.00[CEU][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11070413	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11070414	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11070415	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11070416	0.94[EUR][1000 genomes]
rs11630936	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11631901	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11635039	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11637468	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12439442	0.94[EUR][1000 genomes]
rs12440402	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12442168	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1545182	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16944774	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945686	1.00[CEU][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16950215	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2016840	0.85[JPT][hapmap]
rs2412823	0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs28377221	0.91[EUR][1000 genomes]
rs28438984	0.94[EUR][1000 genomes]
rs28525216	1.00[TSI][hapmap]
rs28542819	0.91[EUR][1000 genomes]
rs28599486	0.94[EUR][1000 genomes]
rs28685813	0.92[EUR][1000 genomes]
rs28706414	0.91[EUR][1000 genomes]
rs2918945	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2918946	0.98[ASN][1000 genomes]
rs3742981	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3850777	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs472797	0.93[ASN][1000 genomes]
rs55927923	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs589649	0.93[ASN][1000 genomes]
rs597705	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs60484809	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs638224	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7178452	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs920339	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9806129	0.94[EUR][1000 genomes]
rs9920164	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
6	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2306674	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs2306674	EPB42	cis	Adipose Subcutaneous	GTEx
rs2306674	ADAL	cis	Nerve Tibial	GTEx
rs2306674	ADAL	cis	Artery Tibial	GTEx
rs2306674	CATSPER2	cis	Esophagus Mucosa	GTEx
rs2306674	TGM5	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44156800-44206400	Weak transcription	Fetal Brain Male	brain
2	chr15:44173600-44208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:44187000-44203600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:44191200-44207400	Weak transcription	Ovary	ovary
7	chr15:44192200-44203600	Weak transcription	Left Ventricle	heart
8	chr15:44192400-44203200	Weak transcription	Right Atrium	heart
9	chr15:44194400-44202000	Weak transcription	NHDF-Ad	bronchial
10	chr15:44194400-44204000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:44194600-44203000	Weak transcription	HMEC	breast
12	chr15:44194600-44203200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:44194600-44208200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:44194800-44200800	Weak transcription	HUVEC	blood vessel
15	chr15:44195000-44200000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:44196200-44198800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:44196400-44198600	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr15:44196400-44203600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:44196400-44203800	Weak transcription	Fetal Heart	heart
20	chr15:44196400-44204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:44196400-44205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:44196400-44207600	Weak transcription	Gastric	stomach
23	chr15:44196400-44208000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:44196400-44212200	Weak transcription	Fetal Stomach	stomach
25	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:44196600-44204600	Weak transcription	Hela-S3	cervix
27	chr15:44196600-44205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:44196600-44208200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr15:44196800-44201800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:44196800-44202400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:44196800-44202400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:44196800-44203000	Weak transcription	Osteobl	bone
33	chr15:44196800-44203600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:44197000-44198600	Strong transcription	Brain Cingulate Gyrus	brain
35	chr15:44197000-44200400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:44197400-44198400	Strong transcription	Brain Angular Gyrus	brain
37	chr15:44197600-44198200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:44197600-44198200	Strong transcription	Brain Germinal Matrix	brain
39	chr15:44197600-44198400	Strong transcription	Brain Anterior Caudate	brain
40	chr15:44197600-44198600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:44197600-44198800	Strong transcription	Brain Hippocampus Middle	brain
42	chr15:44197800-44198200	Enhancers	HepG2	liver
43	chr15:44197800-44198400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:44197800-44198400	Genic enhancers	NHEK	skin
45	chr15:44197800-44198600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:44197800-44198600	Strong transcription	Brain Substantia Nigra	brain
47	chr15:44197800-44198600	Strong transcription	NH-A	brain
48	chr15:44197800-44198600	Strong transcription	NHLF	lung
49	chr15:44197800-44198800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:44197800-44198800	Strong transcription	Fetal Brain Female	brain

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